Change Object Index of Objects in a Collection Instance
Found a workaround. Instead of Index, I'm using the RGB color value from the Object Properties -&gt; Viewport Display of each Collection Instance to drive mix factors in the material of the objects.
From the Object Info node, instead of Object Index, link Color to a SeparateRGB node, and change the Red of the Viewport Color of the instance, same way as you would use Index. Then connect R to Mix node or any other node. Nice thing is you can control each channel separatley, using the Green and Blue value for different things in the same collection instance.
Maybe not as elegant as it should be, but at least for me in the same use case as yours, it does the job.